Landraces ofPhaseolus vulgaris (Fabaceae) in Northern Malawi. I. Regional variation

Bean germplasm collections in northern Malawi revealed the existence of diverse landraces, which have probably been maintained by the local farmers as heterogeneous mixtures since the precolonial introduction of Phaseolus vulgaris into eastern Africa. The various seed types comprising these mixtures are known by an array of local names, reflecting farmer perceptions of seed color and pattern, eating quality, plant structure, origin, and other characteristics. A principal components analysis of morphological, phenological, and agronomic metrical traits for 375 lines randomly selected from 15 landraces revealed a clinal pattern, with the northern and southern areas forming the extremes. Genetic distances, based on the first six PCs, indicated greater between-area variability than within-area variability. Bean landrace diversity in Malawi is likely the result of a complex interplay among forces that generate variability such as outcrossing and human and environmental selection.     

Role of seed flow on the pattern and dynamics of pearl millet (<Emphasis Type="Italic">Pennisetum glaucum</Emphasis> [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger

We studied the regional genetic diversity and seed exchange dynamics of pearl millet landraces in south-western Niger. The genetic study was based on AFLP markers. We found significant genetic differentiation between landraces in different geographical areas of south-western Niger. However, the degree of differentiation was low insofar as only 1.9% of the total molecular diversity was due to regional differentiation, suggesting a relatively high gene flow. Anthropologic studies on farming practices have suggested that seed exchanges between farmers on a large geographical scale probably make a considerable contribution to this result. In order to test this hypothesis, the effects of seed exchange on the genetic diversity of landraces was analyzed on seed samples from two distant villages in contrasting areas of south-western Niger. Seeds imported by farmers into the southern village of Sina Koara did not differ significantly from locally grown landraces. By contrast, in the northern village of Alzou, several samples were genetically different from locally grown landraces and closer to southern accessions. These data suggest that the seed flow is preferentially from south to north, i.e. from an area with more favorable rainfall conditions. The potential consequences for the genetic diversity and adaptation of northern pearl millet landraces are discussed.     

High outcrossing rates in fields with mixed sorghum landraces: how are landraces maintained?

The effect of mating system on genetic diversity is a major theme in plant evolutionary genetics, because gene flow plays a large role in structuring the genetic variability within and among populations. Understanding crop mating systems and their consequences for gene flow can aid in managing agricultural systems and conserving genetic resources. We evaluated the extent of pollen flow, its links with farming practices and its impact on the dynamics of diversity of sorghum in fields of Duupa farmers in Cameroon. Duupa farmers grow numerous landraces mixed in a field, a practice that favours extensive pollen flow. We estimated parameters of the mating system of five landraces representative of the genetic diversity cultivated in the study site, using a direct method based on progeny array. The multilocus outcrossing rate calculated from all progenies was 18% and ranged from 0 to 73% among progenies. Outcrossing rates varied greatly among landraces, from 5 to 40%. Our results also showed that individual maternal plants were usually pollinated by more than eight pollen donors, except for one landrace (three pollen donors). Although the biological traits of sorghum (inflorescence morphology, floral traits, phenology) and the spatial planting practices of Duupa farmers led to extensive pollen flow among landraces, selection exerted by farmers appears to be a key parameter affecting the fate of new genetic combinations from outcrossing events. Because both natural and human-mediated factors shape evolution in crop populations, understanding evolutionary processes and designing in situ conservation measures requires that biologists and anthropologists work together.     

Evidence for maintenance of sex by pathogens in plants

The predominance of outcrossing despite the substantial transmission advantage of self-fertilization remains a paradox. Theory suggests that selection can favor outcrossing if it enables the production of offspring that are less susceptible to pathogen attack than offspring produced via self-fertilization. Thus, if pathogen pressure is contributing to the maintenance of outcrossing in plants, there may be a positive correlation between the number of pathogen species attacking plant species and the outcrossing rate of the plant species. We tested this hypothesis by examining the association between outcrossing rate and the number of fungal pathogen species that attack a large, taxonomically diverse set of seed plants. We show that plant species attacked by more fungal pathogen species have higher outcrossing rates than plants with fewer enemies. This relationship persists after correcting for study bias among natural and agricultural species of plants. We also accounted for the nested hierarchy of relationships among plant lineages by conducting phylogenetically independent contrasts (PICs) within genera and families that were adequately represented in our dataset. A meta-analysis of the correlation between pathogen and outcrossing PICs shows that there is a positive correlation between pathogen species number and outcrossing rates. This pattern is consistent with the hypothesis that pathogen-mediated selection may contribute to the maintenance of outcrossing in species of seed plants.     

Chloroplast DNA evidence for non-random selection of females in an outcrossed population of soybeans [Glycine max (L.)]

Summary Restriction fragment length polymorphisms (RFLPs) were used to assess chloroplast DNA (cpDNA) variation in a population of soybeans subjected to continuous cycles of forced outcrossing. This population was derived by crossing 39 female lines with four male-sterile (Ms₂ms₂) maintainer lines and advancing each generation by selecting only outcrossed seed borne on male-sterile (ms₂ms₂) plants. Analysis of the original 39 female lines revealed three groups based on cpDNA RFLPs. These three groups had been previously documented in soybeans, and the distribution of these groups among the female parents of this population was similar to that observed in germ plasm surveys of soybean. Thirty-four of the female parents had group I cpDNA, 3 had group II, and 2 had group III. Plants collected from this population after seven cycles of outcrossing were scored for four morphological traits (flower color, pubescence color, seed color, and pubescence type) known to be controlled by alleles at single nuclear loci. The frequencies of the phenotypes observed in this study indicated that the population underwent random mating with respect to flower and pubescence color, but deviated from random mating at the other two loci. Analysis of 158 of these same plants collected from the population after seven cycles of outcrossing revealed no individuals with group II or group III cpDNAs. The fixation of the group I cpDNA marker in this outcrossing population was judged to result primarily from selection against individuals in the population with the rare cpDNAs.Published as Paper no. 9640, Journal Series, Nebraska Agric Res Div Project no. 12-187. This research was supported in part by the University of Nebraska-Lincoln Research Council and NIH Biomedical Research Support Grant # RR-07055     

Genetic variation in outcrossing rate and correlated floral traits in a population of grain amaranth (Amaranthus cruentus L.)

The genetic control of breeding system in a population of grain amaranth is described here by the estimates of outcrossing rate variation among individuals and their response to mass selection. In the first generation (S₀), a single morphological marker locus(R/r) controlling plant pigmentation was used for the estimation of outcrossing rate. A mixture of genotypes RR (red) and rr (green) mixed in equal proportions was grown and all rr plants were progeny-tested for estimating the outcrossing rate (t), using the relationship t=H/p, where H = proportion of heterozygotes (Rr) in the progeny, and p = frequency of alleleR. A full range (0 to 100%) of outcrossing rates was found in the first generation, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGabeiDayaara% Gaeyypa0JaaGimaiaac6cacaaIZaGaaGymaiaacYcacqGHGaaicqGH% GaaicuaHdpWCgaqcamaaBaaaleaacaqG0baabeaakiabg2da9iaaic% dacaGGUaGaaGOmaiaaiwdaaaa!441B!\[{\text{\bar t}} = 0.31, \hat \sigma _{\text{t}} = 0.25\], and the distribution was significantly skewed toward high outcrossing.A bidirectional mass selection experiment was initiated for high and low outcrossing rates. In the Hi and Lo lines (Generation S₁), the rate of outcrossing was estimated using the R locus in addition to two other completely dominant morphological markers(B, G1). Relative sex ratios in the monoecious inflorescences of selected lines were estimated by the number of male flowers per glomerule. Outcrossing rate was significantly different between the Hi and Lo lines, and Lo line exhibited much higher male fertility than the Hi line. Such a response to selection indicated a polygenic control of sex expression, and consequently, of the potential for outcrossing in this population. In the second generation (S₂), selection was based on the number of male flowers/glomerule as an index of outcrossing ability. Differences in sex expression between the Hi and Lo lines in S₂ generation had 1.0 male flower/glomerule, while the Hi selection individuals had more or less rectangular distribution from 0.1 to 1.0 male flowers/glomerule.Thus, breeding system in amaranth, as represented by the sex ratios within glomerules and the outcrossing rate parameters, responded to bidirectional selection. Such a genetic component of variation in breeding system has significant implications in the evolution of amaranth species and landraces under domestication.     

Inbreeding and true seed in tetrasomic potato. I. Selfing and open pollination in Andean landraces (Solanum tuberosum Gp. Andigena)

 True potato seed (TPS) may be an alternative method of potato production in developing countries. A breeding method for the sexual propagation of this vegetatively propagated crop should consider the development of parental lines and the type of cultivar to be released. Open-pollinated (OP) cultivars seem to be an inexpensive procedure to produce potato from true seed. However, OP progenies are the result of selfing and outcrossing in male-fertile tetraploid potatoes. The aim of the present research was to establish the effect of inbreeding and open pollination in TPS. Ten Andigena clones were used as parental material to derive hybrid (S₀), inbred (S₁ and S₂), and open-pollinated (OP₁ and OP₂) generations. Significant differences among generations were found for pollen production, pollen viability (as determined by its stainability with aceto-carmine glycerol), number of flowers and berries plant^-1, number of seeds berry^-1, weight of 1000 seeds, and tuber yield plant^-1. The parental populations were significantly different for most of the traits, but not for flower production and berry weight. The interaction of population ×generation was significant for pollen and seed production as well as for weight for 1000 seeds. All the traits evaluated except seed weight showed a strong inbreeding depression, while the OP progenies had intermediate values between the S₀ and the S₁. This demonstrates that open pollination in potatoes is not exclusively the product of selfing; it also results from outcrossing. Received: 10 November 1997 / Accepted: 3 March 1998     

基于神经网络数据挖掘的红色籽用西瓜亲本选择方法研究

根据多年来红色籽用西瓜自交系育种过程中,积累的多代性状复杂、数量庞大的种质资源及数据,利用数据挖掘中的反向传播（Back propagation,BP）神经网络方法,建立红色籽用西瓜BP神经网络模型。以红籽瓜数量性状作为预测依据,选择出具有丰产性状的红籽瓜亲本材料,为育种工作者进行亲本选择时提供一种新的途径和方法。     

元阳3个长期连续栽培水稻地方品种内部遗传异质性分析

水稻地方品种是稻种资源的重要组成部分,遗传多样性十分丰富,具有推广改良品种所缺少或没有的优质种质,是水稻育种和稻种起源、进化研究不可缺少的过渡材料。目前,对水稻地方品种间遗传多样性研究较多,而对其内部异质性研究甚微。本研究用24对微卫星(SSR)引物对云南元阳梯田3个栽种历史悠久的水稻地方品种的内部遗传异质性进行了分析。共检测出117个等位基因,香农指数为红脚老粳居群(0.5911)>白脚老粳A居群(0.4875)>月亮谷居群(0.3070)。结果显示:3个地方品种的内部遗传异质性丰富,且遗传异质性主要得益于个体间,而非居群间。     

Self-fertilization and the escape from pollen limitation in variable pollination environments

Seed production in many plants is pollen limited, likely because of unpredictable variation in the pollinator environment. One way for plants to escape the consequences of pollinator variability is to evolve mating systems, such as autonomous selfing, that assure reproduction without relying on pollinators. We explore this hypothesis through the construction and analysis of heuristic models of plant population dynamics in seed- or site-limited populations. Our analysis suggests several important points: the familiar rule that inbreeding depression greater than 0.5 maintains outcrossing significantly underestimates the threshold required under pollen limited conditions with prior selfing; variability in the pollination environment erodes the ability of inbreeding depression to maintain outcrossing; and variable pollination environments can result in stable intermediate rates of prior selfing. The results reflect the importance of geometric mean fitness (which in a variable environment is less than the arithmetic mean) in the face of temporal variation.     

Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers’ perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F _is over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F _st = 0.36). Historical factors, variation in breeding systems, and farmers’ practices all affected patterns of genetic variation. Farmers’ practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.     

Unlocking the Genetic Diversity of Maize Landraces with Doubled Haploids Opens New Avenues for Breeding

Landraces are valuable genetic resources for broadening the genetic base of elite germplasm in maize. Extensive exploitation of landraces has been hampered by their genetic heterogeneity and heavy genetic load. These limitations may be overcome by the in-vivo doubled haploid (DH) technique. A set of 132 DH lines derived from three European landraces and 106 elite flint (EF) lines were genotyped for 56,110 single nucleotide polymorphism (SNP) markers and evaluated in field trials at five locations in Germany in 2010 for several agronomic traits. In addition, the landraces were compared with synthetic populations produced by intermating DH lines derived from the respective landrace. Our objectives were to (1) evaluate the phenotypic and molecular diversity captured within DH lines derived from European landraces, (2) assess the breeding potential (usefulness) of DH lines derived from landraces to broaden the genetic base of the EF germplasm, and (3) compare the performance of each landrace with the synthetic population produced from the respective DH lines. Large genotypic variances among DH lines derived from landraces allowed the identification of DH lines with grain yields comparable to those of EF lines. Selected DH lines may thus be introgressed into elite germplasm without impairing its yield level. Large genetic distances of the DH lines to the EF lines demonstrated the potential of DH lines derived from landraces to broaden the genetic base of the EF germplasm. The comparison of landraces with their respective synthetic population showed no yield improvement and no reduction of phenotypic diversity. Owing to the low population structure and rapid decrease of linkage disequilibrium within populations of DH lines derived from landraces, these would be an ideal tool for association mapping. Altogether, the DH technology opens new opportunities for characterizing and utilizing the genetic diversity present in gene bank accessions of maize.     

Patterns of population structure in maize landraces from the Central Valleys of Oaxaca in Mexico

Assessing the impact of farmer management of maize landraces in the Central Valleys of Oaxaca, Mexico is crucial to an understanding of maize evolution, as it was first domesticated there. In this paper, we report on the impact of traditional farmer management of maize populations in this region in structuring molecular diversity and on the population dynamics of maize landraces. These populations, from a sample of local landraces cultivated by farmers in six villages, show little among-population differentiation (Fst=0.011). Most surprisingly, there is no isolation by distance and small among-village differentiation (Fst=0.003). For an outbreeding plant such as maize, one would expect populations to fit Hardy-Weinberg equilibrium, but significant homozygote excess (Fis=0.13) was found. This homozygote excess shows remarkable interpopulation and interlocus differences. We show that this pattern is related to variation in the mean anthesis-silking interval as well as to the flowering range or heterogeneity in flowering of a given population. A short anthesis-silking interval and high level of heterogeneity in flowering precocity will favor assortative mating. This leads to a locus-dependent population substructure giving an unusual case of Wahlund effect and inbreeding while high levels of seed exchange among farmers prevent population differentiation at both village and regional levels.     

Mating system of wild Phaseolus lunatus L. and its relationship to population size

Using isozyme variation in a naturally pollinated seed family for 10 wild Phaseolus lunatus L. (Lima bean) populations, ranging in sizes from 10 to 60 reproductive individuals, we estimated levels of outcrossing (t) and parental inbreeding coefficient (F). We also examined the relationship between outcrossing rate and population size. Average estimates of the single-locus outcrossing rate (ts) ranged from 0.024 to 0.246 (mean=0.091+/-0.065). Estimates of the multilocus outcrossing rate (tm) ranged from 0.027 to 0.268, and averaged 0.096+/-0.071. Inbreeding coefficients based on genotypic frequencies of maternal plants were positive and significantly greater than zero (F=0.504), suggesting an excess of homozygotes in all the populations studied. There was indirect evidence of nonrandom mating for outcrosses and this was mainly attributed to self-fertilisation since the averaged difference between tm and ts, which provides a measure of biparental inbreeding, represents only 1% of the autogamy rate. No significant correlation was observed between outcrossing rate and population size. Estimates of t showed significant heterogeneity among populations and factors explaining this tendency are suggested.     

Comparative Effects of Pollen and Seed Migration on the Cytonuclear Structure of Plant Populations. I. Maternal Cytoplasmic Inheritance

We explicitly solve and analyze a series of deterministic continent-island models to delimit the effects of pollen and seed migration on cytonuclear frequencies and disequilibria in random-mating, mixed-mating and self-fertilized populations. Given the critical assumption of maternal cytoplasmic inheritance, five major findings are (i) nonzero cytonuclear disequilibria will be maintained in the island population if and only if at least some migration occurs each generation through seeds with nonrandom cytonuclear associations; (ii) immigrant seeds with no cytonuclear disequilibria can strongly affect the genetic structure of the island population by generating significant and long-lasting transient associations; (iii) with all else being equal, substantially greater admixture disequilibria are generally found with higher rates of seed migration into, or higher levels of self-fertilization within, the island population (with the possible exception of the heterozygote disequilibrium); (iv) pollen migration can either enhance or reduce the cytonuclear disequilibria caused by seed migration, or that due to mixed-mating in the absence of seed migration, but the effect is usually small and appears primarily to make a noticeable difference in predominantly outcrossing populations; and (v) pollen migration alone cannot generate even transient disequilibria de novo in populations with completely random associations. This same basic behavior is exhibited as long as there is some random outcrossing in the island population. Self-fertilized populations represent a special case, however, in that they are necessarily closed to pollen migration, and nonzero disequilibria can be maintained even in the absence of seed migration. All of these general results hold whether the population is censused as adults or as seeds, but the ability to detect nonrandom cytonuclear associations can depend strongly on the life stage censused in populations with a significant level of random outcrossing. We suggest how these models might be used for the estimation of seed and pollen migration.     

Genetic structure of Camellia japonica L. in an old-growth evergreen forest, Tsushima, Japan

The spatial genetic structure of Camellia japonica was investigated, using microsatellite markers, in a 4-ha permanent plot within an old-growth forest. Spatial distribution of individuals was also assessed to obtain an insight into spatial relationships between individuals and alleles. Morisita's index of dispersion showed that 518 C. japonica individuals in the plot were clumped, and Moran's I spatial autocorrelation coefficient revealed weak genetic structure, indicating a low level of allele clustering. Average I correlograms showed that there was stronger genetic structure over short-distance classes. The clumped distribution of individuals and the positive autocorrelation over short-distance classes may result from the limited seed dispersal and microsite heterogeneity of the stand, while the genetic structure may be weakened by overlapping seed shadow and extensive pollen flow, mediated by animal vectors, and the high outcrossing rate found in C. japonica.     

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.     

Alterations in cloned Xenopus ribosomal spacers generated by high-frequency plasmid recombination

In an attempt to understand the mechanisms that have led to the complex intraspecific heterogeneity in spacer organisation found in Xenopus r.DNA, we have transformed Escherichia coli strains that exhibit high levels of plasmid recombination with Xenopus laevis r.DNA sequences inserted in pBR322. We have found that in these recBC sbcA strains, plasmid recombination results in the generation of many types of altered r.DNA spacer at a high frequency. The altered spacers result from two types of deletion/duplication events that occur in the promoter-derived sequences making up much of the spacer. The alterations caused by these events mimic in several ways the different types of organisation found among spacers in the genome. The sbcA-dependent plasmid recombination apparently provides a test system for reconstructing some of the recombinational events that operate during the evolution and maintenance of spacer DNA sequences in vivo.     

Relative impact of mate versus pollinator availability on pollen limitation and outcrossing rates in a mass‐flowering species

Plant mating systems are driven by several pre‐pollination factors, including pollinator availability, mate availability and reproductive traits. We investigated the relative contributions of these factors to pollination and to realized outcrossing rates in the patchily distributed mass‐flowering shrub Rhododendron ferrugineum. We jointly monitored pollen limitation (comparing seed set from intact and pollen‐supplemented flowers), reproductive traits (herkogamy, flower size and autofertility) and mating patterns (progeny array analysis) in 28 natural patches varying in the level of pollinator availability (flower visitation rates) and of mate availability (patch floral display estimated as the total number of inflorescences per patch). Our results showed that patch floral display was the strongest determinant of pollination and of the realized outcrossing rates in this mass‐flowering species. We found an increase in pollen limitation and in outcrossing rates with increasing patch floral display. Reproductive traits were not significantly related to patch floral display, while autofertility was negatively correlated to outcrossing rates. These findings suggest that mate limitation, arising from high flower visitation rates in small plant patches, resulted in low pollen limitation and high selfing rates, while pollinator limitation, arising from low flower visitation rates in large plant patches, resulted in higher pollen limitation and outcrossing rates. Pollinator‐mediated selfing and geitonogamy likely alleviates pollen limitation in the case of reduced mate availability, while reduced pollinator availability (intraspecific competition for pollinator services) may result in the maintenance of high outcrossing rates despite reduced seed production.     

Can females benefit from selfing avoidance? Genetic associations and the evolution of plant gender

Evolutionary stability of dioecy and nuclear gynodioecy in higher plants requires that females produce over twice as many successful seeds as hermaphrodites. This fitness differential is widely thought to derive primarily from the advantages of outcrossing caused by high selfing rates and inbreeding depression in the hermaphrodite. This study hypothesized that (i) extraordinarily high deleterious mutation rates are necessary to double female seed success due to outcrossing, and (ii) the large difference in outcrossing rates between sex morphs causes differential purging of these mutations, resulting in additional genetic selection on male sterility. Using genetically explicit models, I showed that the phenotypic outcrossing advantage requires at least one new highly recessive deleterious mutation per genome per generation, regardless of selection coefficient. However, under this mutational regime, differential purging created strong genetic selection against recessive male sterility that overwhelmed the phenotypic selection in favour of outcrossing. In very small populations and for dominant male sterility, this genetic selection was weaker or absent. This first genetically explicit study of the outcrossing advantage of unisexual females may shed new light on both the genetic and selective conditions for the evolution of gynodioecy and dioecy.